Because several investigations, including genetic studies, have reported associations between serotonin (5-HT) 2A receptor gene and mood disorders, 5-HT 2A receptor gene (HTR2A) is a good candidate gene for the pathophysiology of mood disorders such as major depressive disorder (MDD) and bipolar disorder (BP). Using two functional SNPs (T102C and -A1438G) and two SNPs (rs7997012 and rs1928040) in HTR2A, which reported an association with therapeutic response to the SSRI, we conducted a genetic association analysis of case-control samples (325 MDD patients, 155 BP patients and 802 controls) in the Japanese population. We did not detect significant an association of HTR2A with MDD and BP in allele/genotype-wise or haplotype-wise analysis. In this study, we could detect no evidence of genetic association between 4 markers near HTR2A and mood disorders in the Japanese population, but sample sizes, especially BP, were probably too small to allow a meaningful test.